[Chimera-users] saving charmm layout

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 7 17:10:56 PST 2011

On Mar 7, 2011, at 6:27 AM, Francesco Pietra wrote:

> Hello:
> Is it possible to save pdb conserving as much as possible charmm
> layout (in particular the segments (P1, P2, etc)?  I find speedy to
> edit graphically with Chimera but, afterward, much time is required to
> restore charmm layout.
> thanks
> francesco pietra

Hi Francesco,
	Segment ID is no longer a supported field in the PDB format.  This is  
likely why Chimera isn't preserving your segment information.   
Nonetheless, the columns where segment ID used to be defined (in  
earlier versions of PDB) have nothing defined for them in the current  
PDB version.  Also, the low-level PDB read/write routines in Chimera  
have support for segment ID columns but the upper layers do nothing  
with that support.  So I see no reason why we couldn't add seg-ID- 
preservation to Chimera.  Though it shouldn't be too hard to do I  
nonetheless have quite a few projects on my hands right now, so it may  
be weeks or months before I'm able to get to it.  I will open a  
feature-request ticket for it in our bug database and put you on the  
recipient list so that you'll be notified when it gets implemented.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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